HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization

Mol Cell. 2022 Mar 17;82(6):1225-1238.e6. doi: 10.1016/j.molcel.2022.01.023. Epub 2022 Feb 22.

Abstract

The long-range interactions of cis-regulatory elements (cREs) play a central role in gene regulation. cREs can be characterized as accessible chromatin sequences. However, it remains technically challenging to comprehensively identify their spatial interactions. Here, we report a new method HiCAR (Hi-C on accessible regulatory DNA), which utilizes Tn5 transposase and chromatin proximity ligation, for the analysis of open-chromatin-anchored interactions with low-input cells. By applying HiCAR in human embryonic stem cells and lymphoblastoid cells, we demonstrate that HiCAR identifies high-resolution chromatin contacts with an efficiency comparable with that of in situ Hi-C over all distance ranges. Interestingly, we found that the "poised" gene promoters exhibit silencer-like function to repress the expression of distal genes via promoter-promoter interactions. Lastly, we applied HiCAR to 30,000 primary human muscle stem cells and demonstrated that HiCAR is capable of analyzing chromatin accessibility and looping using low-input primary cells and clinical samples.

Keywords: HiCAR; Silencer-like promoter; chromatin accessibility; chromatin organization; low-input multi-omic.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin* / genetics
  • DNA
  • Gene Expression Regulation
  • Humans
  • Promoter Regions, Genetic
  • Regulatory Sequences, Nucleic Acid*

Substances

  • Chromatin
  • DNA